Research
The Breitbart lab studies viruses and bacteria in a wide range of environments. Here are descriptions of just a few of our many current projects. View recent publications on each of these topics.
Polonies
Gokushovirinae, a subfamily of the Microviridae family, are single-stranded DNA (ssDNA) phages that are ubiquitous in marine environments, but little is known about their diversity and abundance. This knowledge gap is partly due to the methodological limitations associated with studying ssDNA phages. This project focuses on quantifying ssDNA phage abundance and assessing ssDNA phage diversity in the Red Sea through molecular techniques. The polony method is a solid phase PCR that immobilizes the template DNA in an acrylamide gel, then hybridizes the PCR products with a fluorescent probe to determine the abundance of targeted viral groups. Unlike quantitative PCR, the polony approach is compatible with degenerate primer sets, allowing us to quantify the abundance of a diverse group of gokushoviruses instead of targeting a specific subgroup. The gokushovirus major capsid protein was amplified and sequenced from water samples collected from 9 depths (0 m, 20 m, 40 m, 60 m, 80 m, 100 m, 140 m, 200 m, and 400 m) in the Gulf of Aqaba in the Red Sea in September 2015, during a period of water column stratification. Based on the sequences recovered, a probe was designed for the quantification of the gokushoviruses using the polony method. These will provide the first estimates of gokushovirus abundances in the oceans. Insight into the spatiotemporal changes in gokushovirus diversity along with their abundance will elucidate their ecological role in the marine environment.
DNA Barcoding of Fish Eggs
DNA barcoding of fish eggs is a relatively new technique that enables more accurate identification of early life stages of ecologically and economically important fish species. Using DNA barcoding of individual planktonic percomorph eggs, we can determine putative spawning locations of neritic and oceanic fish species in the Gulf of Mexico (GoM). Surveys at 40 stations in the Gulf of Mexico showed a clear delineation of spawning sites, with neritic fish eggs generally found on continental shelves, and oceanic fish eggs found at the surface of deeper waters. However, samples collected between Florida and Cuba revealed exceptions to this trend driven by physical oceanographic processes, with mesoscale eddies transporting eggs of neritic fishes off the Florida continental shelf into the deep Florida Straits. Better understanding of the distribution of fish eggs can help identify regions where additional protection of spawners and recruits may be appropriate.
Submerged Aquatic Vegetation Viral Diversity
Submerged aquatic vegetation (SAV) are plants that live beneath the water’s surface. These plants are taxonomically diverse, including angiosperms, liverworts and macroalgae. Our study focuses on SAV found in the Florida springs & Tampa Bay. Viral-like particles were isolated from each SAV species using chloroform (to kill bacteria), nuclease treatment (to get rid of free nucleic acids), and extraction methods (to break open the viral capsid) to obtain viral nucleic acids, with a focus on single stranded RNA viruses. SAV ecosystems are declining in Florida and we need to figure out why. This project aims to elucidate the role these viruses could play in the health of these ecosystems.
Bacterial & Viral Communities of the Florida Springs
Florida has one of the highest spring densities in the world, with upwards of 7,000 springs. Twenty-three of these are first magnitude springs, which discharge greater than 65 millions gallons of freshwater each day from the Floridan aquifer. The Floridan aquifer is an essential source of drinking water in and around the state. Despite these ecosystems’ importance, there is little is known about the microbial and viral communities which inhabit them. This project assesses the bacterial and viral communities within five Florida springs to understand the compositions of these populations and their spatio-temporal variations.
Ferrojan Horse Hypothesis
Iron (Fe) is an essential micronutrient, required by all living things. However, the bioavailable form of Fe is particularly limited in the marine environment. Fe tends to be speciated into complex forms, including binding to ligands (sticky compounds), rendering it unusable to organisms. Bacteria have developed mechanisms to recruit Fe, for example by using siderophores and cell receptors to bind Fe to their cell surfaces. These receptors have potentially left them vulnerable to the most abundant predator of the oceans, viruses. Viruses that infect bacteria are called bacteriophage (phage). Through data mining it was found that many phage have Fe binding sites on their tail fibers, which was hypothesized as a decoy to allow for phage attachment and infects, similar to a Trojan horse or Ferrojan horse in this case. This project tested the hypothesis in a model organism (E. coli) and now aims to test the hypothesis in the marine environment using Vibrio as a model organism.
MERA
An innovative, beach water quality investigation that considers human behavior, water pollution, and risk of illness. Learn more on the MERA website
Only 10% of the world’s household wastewater is properly treated and disinfected prior to flowing into rivers and ultimately, coastal beaches. Since this wastewater contains millions of pathogens, swimming and playing at beaches polluted by wastewater can greatly impact your health. In total, millions of cases of illness occur each year due to playing at contaminated beaches and this costs the global community 12 billion USD annually. Despite scientific advancements, government beach management approaches rely on outdated compliance practices that do not accurately identify public health risks. This innovative investigation will advance local management practices, serve as an example from a tropical region, as well as contribute to our global achievement of the 2030 Agenda for Sustainable Development. The Investigation MERA research team is composed of anthropologists and natural scientists, from a variety of backgrounds, from Universities, private laboratories, governmental institutions, as well as non-governmental non-profit organizations from the United States of America and Costa Rica. Together, we will execute a holistic beach water quality investigation that will consider human behavior, water pollution, and risk of illness at a Costa Rican beach. Our ultimate goal is to improve beach management and ensure the protection of public health.
Viruses Associated with Harmful Algal Blooms
As part of the USF Center for Red Tide Tracking and Forecasting, the Breitbart lab is using viral metagenomics to identify viruses infecting Karenia brevis, the dinoflagellate that causes Red Tide.
VIDA Seagrass – Viral Infection Dynamics Among Seagrasses
Seagrasses are marine flowering plants (or angiosperms) that create expansive underwater meadows that form the basis of highly productive and valuable ecosystems in coastal oceans. Unlike terrestrial systems where angiosperms dominate plant diversity, seagrasses are the only flowering plants in marine environments. Based on the profound impacts of viral infections on terrestrial plants, viruses are expected to influence seagrass ecology. However, no prior work has investigated viral infection dynamics in seagrasses or the impact of viruses on seagrass health. This project provides fundamental knowledge about seagrass-virus interactions through field and laboratory studies of Thalassia testudinum (i.e., turtlegrass, a climax species and key ecosystem engineer), and turtlegrass virus X (TVX), the only seagrass virus currently reported from experimental research. The lack of a seagrass-virus study system has kept the scientific community from learning which factors drive viral infection in marine angiosperms. By establishing the first seagrass-virus study system, a novel virus-host pathosystem for which virtually nothing is known, this project contributes to a more comprehensive understanding of seagrass ecology and serves as a model for investigating the growing number of seagrass viruses discovered through sequencing efforts.
Seagrass-virus interactions are being investigated through a two-tiered approach involving field studies in Tampa Bay, Florida and microcosm experiments. Field surveys focus on elucidating the nature of turtlegrass-TVX interactions (positive, neutral or negative) and the relationship between turtlegrass genotypic diversity and virus distribution in a natural population where TVX has persisted for at least five years. TVX load is monitored bimonthly over two years to assess how viral load relates to turtlegrass genotype and performance (growth, health, reproductive effort), and abiotic parameters. The investigated turtlegrass meadow contains TVX-positive and negative specimens, thus providing a perfect natural laboratory with homogenous environmental characteristics that allow exploration of the drivers of viral infection. Given that environmental changes may alter host-microbe interactions, complementary microcosm experiments are evaluating turtlegrass responses to TVX infection at the physiological (survival, photochemical capacity, cellular responses) and molecular (transcriptomic) levels in a controlled environment under normal conditions and in the context of salinity changes, an important seagrass stressor. Microcosm experiments also provide the first profiles of seagrass gene expression and measurement of cellular metabolites in response to viral infection. Expected results have direct implications for understanding seagrass production and resilience in the face of global climate change and anthropogenic stress.
VIDA Seagrass is an NSF-funded collaborative project with Cliff Ross (UNF), Dan Martin (UNF), Brad Furman (FWC), Karyna Rosario, and Mya Breitbart (USF).